In the episode, Starbuck returns to the human fleet bearing the Arrow of Apollo. President Laura Roslin leads a team to the surface of Kobol to find the Tomb of Athena and a map to Earth. Commander William Adama overcomes his anger at Roslin and her allies and joins them on Kobol, where the Tomb provides a clue to Earth's location. The fleet is reunited.
In the previous episode, "The Farm", Adama returned to command following an assassination attempt by the Galactica copy of Boomer (Galactica-Boomer). Roslin led almost a third of the fleet back to Kobol to search for a way to Earth. Starbuck left Caprica with Helo and the Cylon known until then as the Caprica copy of Boomer (Sharon).
Roslin struggles to persuade the Quorum of Twelve of Apollo's loyalty. Tom Zarek suggests arming the civilian ships in case Galactica attacks, but Apollo says they would stand no chance against the battlestar. Priestess Elosha reminds everyone that the Scriptures predict that a return to Kobol would result in lives lost.
Starbuck docks with Roslin's flagship. Before she can explain about Caprica-Sharon, Apollo sees her and puts a gun to Caprica-Sharon's head. Helo appears and draws his weapon on Apollo to defend Sharon. Roslin defuses the standoff by promising Sharon will not be harmed but then orders her thrown out the airlock. Roslin only relents when Sharon claims to know the location of the Tomb of Athena, where the Scriptures claim a path to Earth can be found. Roslin threatens to put Helo and Sharon, and thus their unborn child, out the airlock unless Sharon leads them to it.
Privately, Zarek admits to his aide-de-camp, Meier, that he does not share Roslin's religious convictions. They plot to kill Apollo so Zarek can replace him at Roslin's side.
On Kobol, Roslin leads a team that includes Apollo, Starbuck, Sharon, Helo, Zarek, Meier, Elosha, and several guards. Elosha is killed by a land mine. Cylon Centurions ambush the party, who fends them off with the help of Sharon; she grabs a stray grenade launcher and destroys one of the Centurions, to Apollo's surprise.
On Galactica, Commander Adama assesses what resources remain after the defection of part of the fleet to "a religious fanatic and a terrorist", as he describes Roslin and Zarek. He appoints George Birch, an inexperienced but "honest and loyal" pilot, to replace Apollo commanding the Viper pilots; several accidents happen under Birch's leadership. Adama appears before the press; denounces those who followed Roslin, whom he describes as no longer President; and threatens to detain anyone who reports that he does not know where Earth is. Later, he confides in Anastasia "Dee" Dualla how hurt he is by betrayal. Dee replies that he has broken his promise to find the fleet a new home and suggests his hurt has more to do with his own feeling of helplessness than betrayal. Adama dismisses Dee brusquely but later asks for reconnaissance photos of Kobol, promising to reunite the fleet, "our family".